Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water.

Biotransformation High-Throughput Nucleotide Sequencing Hydrocarbons, Brominated / metabolism Rhodopseudomonas / metabolism Transcriptome Water Pollutants, Chemical / metabolism
Biotransformation Dehalogenase Genome Hexabromocyclododecane Purple photosynthetic bacterium

Journal

The Science of the total environment
ISSN: 1879-1026
Titre abrégé: Sci Total Environ
Pays: Netherlands
ID NLM: 0330500

Informations de publication

Date de publication:
20 Nov 2019
Historique:
received: 03 05 2019
revised: 04 07 2019
accepted: 10 07 2019
pubmed: 28 7 2019
medline: 14 1 2020
entrez: 27 7 2019
Statut: ppublish

Résumé

We discovered one purple photosynthetic bacterium, Rhodopseudomonas palustris YSC3, which has a specific ability to degrade 1, 2, 5, 6, 9, 10-hexabromocyclododecane (HBCD). The whole transcriptome of R. palustris YSC3 was analyzed using the RNA-based sequencing technology in illumina and was compared as well as discussed through Multi-Omics onLine Analysis System (MOLAS, http://molas.iis.sinica.edu.tw/NTUIOBYSC3/) platform we built. By using genome based mapping approach, we can align the trimmed reads on the genome of R. palustris and estimate the expression profiling for each transcript. A total of 341 differentially expressed genes (DEGs) in HBCD-treated R. palustris (RPH) versus control R. palustris (RPC) was identified by 2-fold changes, among which 305 genes were up-regulated and 36 genes were down-regulated. The regulated genes were mapped to the database of Gene Ontology (GO) and Genes and Genomes Encyclopedia of Kyoto (KEGG), resulting in 78 pathways being identified. Among those DEGs which annotated to important functions in several metabolic pathways, including those involved in two-component system (13.6%), ribosome assembly (10.7%), glyoxylate and dicarboxylate metabolism (5.3%), fatty acid degradation (4.7%), drug metabolism-cytochrome P450 (2.3%), and chlorocyclohexane and chlorobenzene degradation (3.0%) were differentially expressed in RPH and RPC samples. We also identified one transcript annotated as dehalogenase and other genes involved in the HBCD biotransformation in R. palustris. Furthermore, the putative HBCD biotransformation mechanism in R. palustris was proposed.

Identifiants

DOI: 10.1016/j.scitotenv.2019.07.140 PMID: 31349166
pubmed: 31349166
pii: S0048-9697(19)33253-X
doi: 10.1016/j.scitotenv.2019.07.140
pii:
doi:

Substances chimiques

Hydrocarbons, Brominated 0
Water Pollutants, Chemical 0
hexabromocyclododecane 5I9835JO3M

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

249-258

Informations de copyright

Copyright © 2019 Elsevier B.V. All rights reserved.

Auteurs

Reuben Wang (R)

Department of Food Science, Tunghai University, Taiwan, No.1727, Sec.4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan.

Chung-Yen Lin (CY)

Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan.

Shu-Hwa Chen (SH)

Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan.

Kai-Jiun Lo (KJ)

Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan.

Chi-Te Liu (CT)

Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan.

Tzu-Ho Chou (TH)

Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.

Yang-Hsin Shih (YH)

Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. Electronic address: yhs@ntu.edu.tw.

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Classifications MeSH

questionsmedicales.fr › Phénomènes physiologiques › Phénomènes pharmacologiques et toxicologiques › Pharmacocinétique › Biotransformation › Using high-throughput transcriptome sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Using high-throughput transcriptome sequencing...
questionsmedicales.fr › Composés chimiques organiques › Hydrocarbures › Hydrocarbures halogénés › Hydrocarbures bromés › Using high-throughput transcriptome sequencing...
questionsmedicales.fr › Bactéries › Proteobacteria › Alphaproteobacteria › Bradyrhizobiaceae › Rhodopseudomonas › Using high-throughput transcriptome sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Using high-throughput transcriptome sequencing...
questionsmedicales.fr › Actions chimiques et utilisations › Actions toxiques › Polluants environnementaux › Polluants de l'eau › Polluants chimiques de l'eau › Using high-throughput transcriptome sequencing...